Strain identifier

BacDive ID: 15425

Type strain: Yes

Species: Streptomyces nitrosporeus

Strain Designation: 0-20

Strain history: KCC S-0064 <-- Y. Okami O-20 (NIHJ 21).

NCBI tax ID(s): 28894 (species)

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General

@ref: 9223

BacDive-ID: 15425

DSM-Number: 40023

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic

description: Streptomyces nitrosporeus 0-20 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 28894
  • Matching level: species

strain history

@refhistory
9223<- E.B. Shirling, ISP <-Y. Okami, 0-20
67770KCC S-0064 <-- Y. Okami O-20 (NIHJ 21).

doi: 10.13145/bacdive15425.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Streptomyces
  • species: Streptomyces nitrosporeus
  • full scientific name: Streptomyces nitrosporeus Okami 1952 (Approved Lists 1980)

@ref: 9223

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces nitrosporeus

full scientific name: Streptomyces nitrosporeus Okami 1952

strain designation: 0-20

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
125439positive99.6
12543990.7no
12543891no
125438positive91.476

colony morphology

@refcolony colorincubation periodmedium used
19388Ivory10-14 daysISP 2
19388Ivory10-14 daysISP 3
19388Ivory10-14 daysISP 4
1938810-14 daysISP 5
1938810-14 daysISP 6
1938810-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19388yesAerial MyceliumLight greyISP 2
19388yesAerial MyceliumLight greyISP 3
19388yesAerial MyceliumLight greyISP 4
19388yesAerial MyceliumLight greyISP 5
19388yesAerial MyceliumLight greyISP 6
19388yesAerial MyceliumGreyISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9223GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19388ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19388ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19388ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19388ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19388ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19388ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
9223STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

culture temp

@refgrowthtypetemperature
19388positiveoptimum30
9223positivegrowth28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
125438aerobe92.254
125439facultative anaerobe97.2

spore formation

@refspore descriptionspore formationconfidence
19388Formation of spore chains: rectiflixibilis, spore surface: smoothyes
125439yes92.1
125438yes92.592

compound production

@refcompound
9223nitrosporin
20216Nitrosporin
67770Nitrosporin

halophily

  • @ref: 19388
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1938862968cellulose-
1938816634raffinose-
1938826546rhamnose-
1938828757fructose-
1938829864mannitol-
1938817268myo-inositol-
1938818222xylose-
1938817992sucrose-
1938822599arabinose+/-
1938817234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368arginine dihydrolase+3.5.3.6
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368lysine decarboxylase+4.1.1.18
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19388+++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
9223garden soilJapanJPNAsia
67770Humus soilJapanJPNAsiaTokyo

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

taxonmaps

  • @ref: 69479
  • File name: preview.99_135.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_120;99_135&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: JQ924413
  • Sequence Identity:
  • Total samples: 4030
  • soil counts: 2441
  • aquatic counts: 286
  • animal counts: 1009
  • plant counts: 294

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
92231Risk group (German classification)
193881Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces nitrosporeus strain CGMCC 4.1973 clone 1 16S ribosomal RNA gene, complete sequenceJQ9244111478nuccore28894
20218Streptomyces nitrosporeus strain CGMCC 4.1973 clone 3 16S ribosomal RNA gene, complete sequenceJQ9244121478nuccore28894
20218Streptomyces nitrosporeus strain CGMCC 4.1973 clone 4 16S ribosomal RNA gene, complete sequenceJQ9244131478nuccore28894
20218Streptomyces nitrosporeus gene for 16S rRNA, partial sequenceAB122747564nuccore28894
20218Streptomyces nitrosporeus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4064D43996120nuccore28894
20218Streptomyces nitrosporeus gene for 16S rRNA, partial sequence, strain: NBRC 12803AB1841591468nuccore28894
20218Streptomyces nitrosporeus gene for 16S rRNA, partial sequence, strain: NBRC 3362AB1847511475nuccore28894
20218Streptomyces nitrosporeus strain NRRL B-1316 16S ribosomal RNA gene, partial sequenceEF1786801487nuccore28894

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces nitrosporeus ATCC 12769GCA_008704555completencbi28894
66792Streptomyces nitrosporeus JCM 4598GCA_014650375scaffoldncbi28894
66792Streptomyces nitrosporeus strain ATCC 1276928894.3completepatric28894
66792Streptomyces nitrosporeus strain JCM 459828894.4wgspatric28894

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.476no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.889no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes92.254no
125438spore-formingspore-formingAbility to form endo- or exosporesyes92.592yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.8no
125438motile2+flagellatedAbility to perform flagellated movementno91no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes92.1
125439BacteriaNetmotilityAbility to perform movementno90.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative anaerobe97.2

External links

@ref: 9223

culture collection no.: DSM 40023, ATCC 12769, ATCC 19792, CBS 544.68, DSM 41158, ETH 24344, ETH 24415, HUT 6032, IFO 12803, IFO 3362, IMRU 3728, ISP 5023, JCM 4064, KCC S-0064, KCC S-0598, KCTC 9761, NBRC 12803, NBRC 3362, RIA 1071, PSA 206, BCRC 13645, CGMCC 4.1973, JCM 4598, NCIMB 9717, NRRL B-1316, RIA 503, VKM Ac-1191, VKM Ac-1202

straininfo link

  • @ref: 84512
  • straininfo: 35657

literature

  • topic: Phylogeny
  • Pubmed-ID: 25663056
  • title: Streptomyces maoxianensis sp. nov., a novel actinomycete isolated from soil in Maoxian, China.
  • authors: Guan X, Liu C, Zhao J, Fang B, Zhang Y, Li L, Jin P, Wang X, Xiang W
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-015-0403-9
  • year: 2015
  • mesh: Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phospholipids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9223Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40023)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40023
19388Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40023.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
84512Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID35657.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1